Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1732 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1216348665 sf1216345961 12 16348665 1.28E-18 NA
vg1016081589 sf1016010361 10 16081589 1.84E-18 NA
vg1016228595 sf1016157367 10 16228595 4.10E-18 2.72E-06
vg0309337354 sf0309336290 3 9337354 5.14E-18 NA
vg0726879159 sf0726878165 7 26879159 6.00E-18 NA
vg1215474654 sf1215471951 12 15474654 7.10E-18 2.61E-06
vg0129864447 sf0129863402 1 29864447 8.39E-18 NA
vg1217055950 sf1217049905 12 17055950 1.88E-16 NA
vg0906778436 sf0906777436 9 6778436 NA 1.55E-06
vg0107647091 sf0107646091 1 7647091 NA 2.34E-06